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5 results on '"Jenkins, Kylie"'

1. Effect of ten-valent pneumococcal conjugate vaccine introduction on pneumonia hospital admissions in Fiji: a time-series analysis

Author

Reyburn, Rita, Tuivaga, Evelyn, Nguyen, Cattram D, Ratu, Felisita T, Nand, Devina, Kado, Joe, Tikoduadua, Lisi, Jenkins, Kylie, de Campo, Margaret, Kama, Mike, Devi, Rachel, Rafai, Eric, Weinberger, Daniel M, Mulholland, E Kim, and Russell, Fiona M

Abstract

BACKGROUND: In October, 2012, Fiji introduced routine infant immunisation with a ten-valent pneumococcal conjugate vaccine (PCV10) using three primary doses and no booster dose (3 + 0 schedule). Data are scarce for the effect of PCV in the Asia and Pacific region. We aimed to evaluate the effect of PCV10 on pneumonia hospital admissions in children younger than 5 years and adults aged 55 years and older in Fiji, 5 years after vaccine introduction. METHODS: We did a time-series analysis assessing changes in pneumonia hospital admissions at three public tertiary hospitals in Fiji. Four pneumonia outcomes were evaluated: all-cause pneumonia, severe or very severe pneumonia, hypoxic pneumonia, and radiological pneumonia. Participants aged younger than 2 months, 2-23 months, 24-59 months, and 55 years and older were included. Data were extracted from the national hospital admission database according to International Classification of Diseases-tenth revision codes J10·0-18·9, J21, and J22 for all-cause pneumonia. Medical records and chest radiographs were reviewed for the main tertiary hospital to reclassify hospital admissions in children aged younger than 2 years as severe or very severe, hypoxic, or radiological pneumonia as per WHO definitions. Time-series analyses were done using the synthetic control method and multiple imputation to adjust for changes in hospital usage and missing data. FINDINGS: Between Jan 1, 2007, and Dec 31, 2017, the ratio of observed cases to expected cases for all-cause pneumonia was 0·92 (95% CI 0·70-1·36) for children aged younger than 2 months, 0·86 (0·74-1·00) for children aged 2-23 months, 0·74 (0·62-0·87) for children aged 24-59 months, and 1·90 (1·53-2·31) in adults aged 55 years and older, 5 years after PCV10 introduction. These findings indicate a reduction in all-cause pneumonia among children aged 24-59 months and an increase in adults aged 55 years and older, but no change among children aged younger than 2 months. Among children aged 2-23 months, we observed declines of 21% (95% CI 5-35) for severe or very severe pneumonia, 46% (33-56) for hypoxic pneumonia, and 25% (9-38) for radiological pneumonia. Mortality reduced by 39% (95% CI 5-62) for all-cause pneumonia, bronchiolitis, and asthma admissions in children aged 2-23 months. INTERPRETATION: The introduction of PCV10 was associated with a decrease in pneumonia hospital admissions in children aged 2-59 months. This is the first study in a middle-income country in the Asia and Pacific region to show the effect of PCV on pneumonia, filling gaps in the literature on the effects of PCV10 and 3 + 0 schedules. These data support decision making on PCV introduction for other low-income and middle-income countries in the region. FUNDING: Department of Foreign Affairs and Trade of the Australian Government.

Published
2020

2. Epidemiology and risk factors for typhoid fever in Central Division, Fiji, 2014-2017: A case-control study

Author

Prasad, Namrata, Jenkins, Aaron P, Naucukidi, Lanieta, Rosa, Varanisese, Sahu-Khan, Aalisha, Kama, Mike, Jenkins, Kylie M, Jenney, Adam WJ, Jack, Susan J, Saha, Debasish, Horwitz, Pierre, Jupiter, Stacy D, Strugnell, Richard A, Mulholland, E Kim, and Crump, John A

Subjects
lcsh:Arctic medicine. Tropical medicine, lcsh:RC955-962, lcsh:Public aspects of medicine, lcsh:RA1-1270
Abstract

BACKGROUND: Typhoid fever is endemic in Fiji, with high reported annual incidence. We sought to identify the sources and modes of transmission of typhoid fever in Fiji with the aim to inform disease control. METHODOLOGY/PRINCIPAL FINDINGS: We identified and surveyed patients with blood culture-confirmed typhoid fever from January 2014 through January 2017. For each typhoid fever case we matched two controls by age interval, gender, ethnicity, and residential area. Univariable and multivariable analysis were used to evaluate associations between exposures and risk for typhoid fever. We enrolled 175 patients with typhoid fever and 349 controls. Of the cases, the median (range) age was 29 (2-67) years, 86 (49%) were male, and 84 (48%) lived in a rural area. On multivariable analysis, interrupted water availability (odds ratio [OR] = 2.17; 95% confidence interval [CI] 1.18-4.00), drinking surface water in the last 2 weeks (OR = 3.61; 95% CI 1.44-9.06), eating unwashed produce (OR = 2.69; 95% CI 1.48-4.91), and having an unimproved or damaged sanitation facility (OR = 4.30; 95% CI 1.14-16.21) were significantly associated with typhoid fever. Frequent handwashing after defecating (OR = 0.57; 95% CI 0.35-0.93) and using soap for handwashing (OR = 0.61; 95% CI 0.37-0.95) were independently associated with a lower odds of typhoid fever. CONCLUSIONS: Poor sanitation facilities appear to be a major source of Salmonella Typhi in Fiji, with transmission by drinking contaminated surface water and consuming unwashed produce. Improved sanitation facilities and protection of surface water sources and produce from contamination by human feces are likely to contribute to typhoid control in Fiji.

Published
2018

3. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

Author

Wong, Vanessa K., Baker, Stephen, Connor, Thomas R., Pickard, Derek, Page, Andrew J., Dave, Jayshree, Murphy, Niamh, Holliman, Richard, Sefton, Armine, Millar, Michael, Dyson, Zoe A., Dougan, Gordon, Holt, Kathryn E., Parkhill, Julian, Feasey, Nicholas A., Kingsley, Robert A., Thomson, Nicholas R., Keane, Jacqueline A., Weill, François- Xavier, Le Hello, Simon, Hawkey, Jan, Edwards, David, Harris, Simon R., Cain, Amy K., Hadfield, James, Hart, Peter J., Thieu, Nga Tran Vu, Klemm, Elizabeth, Breiman, Robert F., Watson, Conall H., Edmunds, W. John, Kariuki, Samuel, Gordon, Melita A., Heyderman, Robert S., Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Msefula, Chisomo, Chabalgoity, Jose A., Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A., Dolecek, Christiane, Keddy, Karen H., Smith, Anthony M., Parry, Christopher M., Karkey, Abhilasha, Dongol, Don, Basnyat, Buddha, Arjyal, Amit, Mulholland, E. Kim, Campbell, James I., Dufour, Muriel, Bandaranayake, Don, Toleafoa, Take N., Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul, Dance, David, Davong, Viengmon, Onsare, Robert S., Isaia, Lupeoletalalelei, Thwaites, Guy, Wijedoru, Lalith, Crump, John A., de Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J., Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Mather, Alison E., Amos, Ben, Addenbrooke's Hospital, Cambridge University NHS Trust, The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine (LSHTM), University of Oxford [Oxford], Cardiff University, Barts Health NHS Trust [London, UK], Centre for Sytems Genomics, University of Melbourne, Department of Engineering [Cambridge], University of Cambridge [UK] (CAM), Liverpool School of Tropical Medicine (LSTM), University of Liverpool, Institute of Food Research [Norwich], Institute for Astronomy [Honolulu], University of Hawai‘i [Mānoa] (UHM), Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris], Atmospheric Chemistry Observations and Modeling Laboratory (ACOML), National Center for Atmospheric Research [Boulder] (NCAR), INM-8, Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, Global Disease Detection Division, Centers for Disease Control and Prevention, Department of Applied Mathematics and Theoretical Physics (DAMTP), University College of London [London] (UCL), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institut National de Recherche Biomédicale [Kinshasa] (INRB), University of Malawi, Universidad de la República [Montevideo] (UCUR), IHU-LIRYC, Université Bordeaux Segalen - Bordeaux 2-CHU Bordeaux [Bordeaux], Department of Mathematics and Statistics [Toronto], York University [Toronto], Department of Mathematical Sciences [Varanasi], Banaras Hindu University [Varanasi] (BHU), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Public Health England [London], Nuffield Department of Clinical Medicine [Oxford], This work was supported by a number of organizations. The Wellcome Trust Sanger Institute authors were funded by Wellcome Trust Award #098051. V.K.W. was supported by the Wellcome Trust (#098051) and the National Institute of HealthResearch (NIHR) Cambridge Biomedical Research Centre (BRC). N.F. was supported by the Wellcome Trust Research Fellowship #WT092152MA. N.F., R.S.H. and this work were supported by a strategic award from the Wellcome Trust for the MLW ClinicalResearch Programme (#101113/Z/13/Z). C.P. was funded by The Wellcome Trust Mahidol University Oxford Tropical Medicine Research Programme, supported by the Wellcome Trust of Great Britain (Major Overseas Programmes—Thailand Unit CoreGrant), the European Society for Paediatric Infectious Diseases and University of Oxford-Li Ka Shing Global Health Foundation. D.D., P.N. and V.D. were supported by the Wellcome Trust (core grant #089275/H/09/Z). Z.A.D. was supported by the WellcomeTrust (Strategic award #106158). K.E.H. was supported by the NHMRC of Australia (fellowship #1061409) and the Victorian Life Sciences Computation Initiative (VLSCI, grant #VR0082). C.A.M. was supported by a Clinical Research Fellowship fromGlaxoSmithKline and PJH by a UK Medical Research Council PhD studentship. This work forms part of an EU FP7 Marie Curie Actions Industry Academia Partnerships and Pathways (IAPP) Consortium Programme, entitled GENDRIVAX (Genome-drivenvaccine development for bacterial infections), involving the Wellcome Trust Sanger Institute, KEMRI Nairobi and Novartis Vaccines Institute for Global Health. The Institut Pasteur (IP) authors were funded by the IP, the Institut de Veille Sanitaire and by theFrench Government ‘Investissement d’Avenir’ programme (Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence, grant #ANR-10-LABX-62-IBEID). C.H.W. was supported by the UK Medical Research Council (MRC, MR/J003999/1).C.O. was supported by Society in Science, The Branco Weiss Fellowship, administered by the ETH Zurich. A.K.C. was supported by the MRC (#G1100100/1). J.J. was supported by the antibiotic resistance surveillance project in DR Congo, funded by Project 2.01 of the Third Framework Agreement between the Belgian Directorate General of Development Cooperation and the Institute of Tropical Medicine, Antwerp, Belgium. F.M. was supported by a research grant from the Bill and Melinda Gates Foundation. J.A.C. was supported by the joint US National Institutes of Health-National Science Foundation Ecology and Evolution of Infectious Disease program (#R01 TW009237) and the UK Biotechnology and Biological Sciences Research Council (BBSRC, BB/J010367/1), and by UK BBSRC Zoonoses in Emerging Livestock Systems awards #BB/L017679, #BB/L018926 and #BB/L018845. S.K. was supported by the NIH Grant Number R01 AI099525-02. S.B. is a Sir Henry Dale Fellow, jointly funded by the Wellcome Trust and the Royal Society (#100087/Z/12/Z). S.O. was supported by the National Institute Of Allergy And Infectious Diseases of the National Institutes of Health (#R01AI097493). C.D. was supported by the University of Oxford-Li Ka Shing Global Health Programme. A.E.M. was supported by a Biotechnology and Biological Sciences Research Councilaward (#BB/M014088/1). P.T. was supported by the Wellcome Trust of Great Britain (Major Overseas Programmes—Thailand Unit Core Grant) and University of Oxford-Li Ka Shing Global Health Foundation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Dyson, Zoe A [0000-0002-8887-3492], Holt, Kathryn E [0000-0003-3949-2471], Apollo - University of Cambridge Repository, University of Oxford, Biotechnology and Biological Sciences Research Council (BBSRC), Institut Pasteur [Paris] (IP), and Universidad de la República [Montevideo] (UDELAR)

Subjects
0301 basic medicine, DNA, Bacterial, Genotype, Science, Population, General Physics and Astronomy, Biology, Salmonella typhi, complex mixtures, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Typhoid fever, Article, 03 medical and health sciences, medicine, Cluster Analysis, Humans, Typhoid Fever, education, Genotyping, Phylogeny, Genetics, education.field_of_study, Multidisciplinary, Geography, business.industry, Haplotype, Subclade, General Chemistry, Sequence Analysis, DNA, medicine.disease, bacterial infections and mycoses, 3. Good health, Biotechnology, 030104 developmental biology, Haplotypes, Microbial genetics, bacteria, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business
Abstract

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations., Typhoid fever is caused by Salmonella enterica serovar Typhi (S. Typhi). This study examines ∼2,000 clinical isolates of S. Typhi to show highly structured/geographically restricted genomes except rapidly disseminating H58 subclade, and design a genotyping framework for tracking the disease.

Published
2016

4. A cross-sectional seroepidemiological survey of typhoid fever in Fiji

Author

Watson, Conall H, Baker, Stephen, Lau, Colleen L, Rawalai, Kitione, Taufa, Mere, Coriakula, Jerimaia, Thieu, Nga Tran Vu, Van, Tan Trinh, Ngoc, Dung Tran Thi, Hens, Niel, Lowry, John H, De Alwis, Ruklanthi, Cano, Jorge, Jenkins, Kylie, Mulholland, E Kim, Nilles, Eric J, Kama, Mike, and Edmunds, W John

Subjects
Adult, Male, Adolescent, Young Adult, Age Distribution, Seroepidemiologic Studies, Surveys and Questionnaires, Odds Ratio, Fiji, Humans, Sanitation, Sex Distribution, Typhoid Fever, Child, Aged, Demography, Vaccination, Infant, Middle Aged, Salmonella typhi, Antibodies, Bacterial, 3. Good health, FOS: Sociology, Cross-Sectional Studies, Logistic Models, Socioeconomic Factors, Child, Preschool, Immunoglobulin G, Multivariate Analysis, Female
Abstract

Fiji, an upper-middle income state in the Pacific Ocean, has experienced an increase in confirmed case notifications of enteric fever caused by Salmonella enterica serovar Typhi (S. Typhi). To characterize the epidemiology of typhoid exposure, we conducted a cross-sectional sero-epidemiological survey measuring IgG against the Vi antigen of S. Typhi to estimate the effect of age, ethnicity, and other variables on seroprevalence. Epidemiologically relevant cut-off titres were established using a mixed model analysis of data from recovering culture-confirmed typhoid cases. We enrolled and assayed plasma of 1787 participants for anti-Vi IgG; 1,531 of these were resident in mainland areas that had not been previously vaccinated against S. Typhi (seropositivity 32.3% (95%CI 28.2 to 36.3%)), 256 were resident on Taveuni island, which had been previously vaccinated (seropositivity 71.5% (95%CI 62.1 to 80.9%)). The seroprevalence on the Fijian mainland is one to two orders of magnitude higher than expected from confirmed case surveillance incidence, suggesting substantial subclinical or otherwise unreported typhoid. We found no significant differences in seropositivity prevalences by ethnicity, which is in contrast to disease surveillance data in which the indigenous iTaukei Fijian population are disproportionately affected. Using multivariable logistic regression, seropositivity was associated with increased age (odds ratio 1.3 (95% CI 1.2 to 1.4) per 10 years), the presence of a pit latrine (OR 1.6, 95%CI 1.1 to 2.3) as opposed to a septic tank or piped sewer, and residence in settlements rather than residential housing or villages (OR 1.6, 95% CI 1.0 to 2.7). Increasing seropositivity with age is suggestive of low-level endemic transmission in Fiji. Improved sanitation where pit latrines are used and addressing potential transmission routes in settlements may reduce exposure to S. Typhi. Widespread unreported infection suggests there may be a role for typhoid vaccination in Fiji, in addition to public health management of cases and outbreaks.

5. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

Author

Wong, Vanessa K, Baker, Stephen, Pickard, Derek J, Parkhill, Julian, Page, Andrew J, Feasey, Nicholas A, Kingsley, Robert A, Thomson, Nicholas R, Keane, Jacqueline A, Weill, François-Xavier, Edwards, David J, Hawkey, Jane, Harris, Simon R, Mather, Alison E, Cain, Amy K, Hadfield, James, Hart, Peter J, Thieu, Nga Tran Vu, Klemm, Elizabeth J, Glinos, Dafni A, Breiman, Robert F, Watson, Conall H, Kariuki, Samuel, Gordon, Melita A, Heyderman, Robert S, Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Edmunds, W John, Msefula, Chisomo, Chabalgoity, Jose A, Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A, Dolecek, Christiane, Keddy, Karen H, Smith, Anthony M, Parry, Christopher M, Karkey, Abhilasha, Mulholland, E Kim, Campbell, James I, Dongol, Sabina, Basnyat, Buddha, Dufour, Muriel, Bandaranayake, Don, Naseri, Take Toleafoa, Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul, Onsare, Robert S, Isaia, Lupeoletalalei, Dance, David, Davong, Viengmon, Thwaites, Guy, Wijedoru, Lalith, Crump, John A, De Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J, Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Holt, Kathryn E, and Dougan, Gordon

Subjects
Phylogeography, Drug Resistance, Multiple, Bacterial, Molecular Sequence Data, Quinolines, Humans, Sequence Analysis, DNA, Salmonella typhi, Typhoid Fever, Genome, Bacterial, Phylogeny, 3. Good health, Anti-Bacterial Agents
Abstract

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.

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